Biodiversity is thought to regulate a wide range of agroecosystem processes including plant production and disease suppression. Farmers have used crop rotations, a form of biodiversity, for thousands of years and this may be due, in part, to early observations of 'disease prevention' in the form of increased yield. However, the evidence for a mechanistic link between crop rotations and disease suppression has not yet been elucidated. Disease suppressive soils are characterized by the biocontrol properties provided by resident soil microorganisms. Biocontrol properties include antibiosis via production of antifungal or antibacterial compounds known to suppress the growth of soil-borne pathogens. In this study, we investigated the impact of long-term crop diversity (via rotation) on microbial communities and disease suppressive functional potential in soils. We hypothesized that plant and microbial biodiversity provide disease suppressive functions in soils. To address these hypotheses, we collected soil samples from a 12-year crop rotation experiment at the Kellogg Biological Station Long-Term Ecological Research (KBS LTER) site. We sampled seven treatments along a crop diversity gradient (monoculture to five crop species) and a spring fallow (naturally regenerating plants) treatment to examine the influence of crop diversity on total bacterial community composition (16S rRNA gene sequencing) and a subset of microorganisms capable of producing antifungal compounds (2,4-diacetylphloroglucinol: phlD gene fingerprint analysis; pyrrolnitrin: prnD gene quantitative PCR). Our study revealed that crop diversity significantly influenced bacterial community composition, and crop rotations decreased bacterial diversity by 4% on average compared to monocultures. Crop rotations did, however, increase disease suppressive functional group prnD gene abundance in the more diverse rotation (corn-soybean-wheat + cover crops) by about 9% compared to monocultures. Variation in plant inputs to soil organic matter pools may be a possible mechanism driving shifts in microbial community patterns and disease suppressive functional potential.